Package: methVisual

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch methVisual_1.4.0.tar.gz

StartedAt: 2011-10-20 16:01:53 -0700 (Thu, 20 Oct 2011)

EndedAt: 2011-10-20 16:04:11 -0700 (Thu, 20 Oct 2011)

EllapsedTime: 138.5 seconds

RetCode: 0

Status:  OK

CheckDir: methVisual.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/methVisual.Rcheck'
* using R version 2.13.2 (2011-09-30)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'methVisual/DESCRIPTION' ... OK
* this is package 'methVisual' version '1.4.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'methVisual' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under inst/doc ... NOTE
  'qpdf' made some significant size reductions:
     compacted 'methVisual.pdf' from 352Kb to 210Kb
  consider running tools::compactPDF() on these files
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package 'methVisual' ...
** R
** data
** inst
** preparing package for lazy loading
Warning in rgl.init(initValue) : RGL: GLX extension missing on server
Warning in fun(...) : error in rgl_init
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
Warning messages:
1: In rgl.init(initValue) : RGL: GLX extension missing on server
2: In fun(...) : error in rgl_init

* DONE (methVisual)

name	user	system	elapsed
Cooccurrence	0.805	0.029	0.860
MethAlignNW	2.654	0.067	2.925
MethDataInput	0.055	0.018	0.141
MethLollipops	0.015	0.001	0.017
MethylQC	2.125	0.046	2.324
cgInAlign	0.003	0.001	0.004
cgMethFinder	0.001	0.000	0.001
coversionGenom	0.000	0.000	0.001
findNonAligned	0.003	0.002	0.006
heatMapMeth	0.122	0.005	0.127
makeDataMethGFF	0.489	0.030	0.755
makeLocalExpDir	0.048	0.019	0.169
makeTabFilePath	0.006	0.002	0.038
matrixSNP	0.459	0.018	0.517
methCA	0.020	0.003	0.024
methData	0.003	0.001	0.003
methFisherTest	0.054	0.003	0.059
methWhitneyUTest	0.007	0.001	0.008
plotAbsMethyl	0.004	0.001	0.006
plotMatrixSNP	0.960	0.026	1.003
readBisulfFASTA	0.051	0.018	0.076
selectRefSeq	0.048	0.020	0.109